Thursday, July 28, 2011

When Charles Darwin introduced his theory of evolution he explained how it could be tested. As the sage of Kent explained:

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.

While providing a test of falsification sounds scientific, this was just another one of Darwin’s protectionist moves. For in science, theories should be tested against realistic criteria, not universal negatives. How could a scientist, who is skeptical of the notion that all of biology spontaneously arose on its own, prove that a biological structure “could not possibly have been formed by numerous, successive, slight modifications.”

Biology is chocked full of such structures, but there is a catch. Darwin was requiring that the skeptic prove that such structures “could not possibly” have evolved. Given the evolutionist’s liberal use of imaginative just-so stories, this requirement would seem practically impossible.

Darwin was not looking for examples that show evolution to be unlikely. He did not say “did not likely” evolve. He said “could not possibly” evolve. Darwin was erecting high walls around his idea.

Nonetheless, Darwin’s defensive strategy was doomed to fail. The idea is so scientifically flawed that even its own Maginot Line could not save it. Today, the question is not is there a structure that “could not possibly” have evolved, but rather which one of the thousands and thousands of examples in biology should we pick? In recent years proteins have provided yet another army of examples where even the evolutionist’s own numbers show a twenty seven order of magnitude shortfall between expectations and reality.

What is interesting about all this is not that evolution is riddled with failures, but the denial that is universal amongst evolutionists. In fact, evolutionists not only deny there is any problem, they insist evolution is a fact, beyond a shadow of a doubt.

Some wonder why the failure of Darwin’s own Maginot Line left evolution unharmed. How could evolution be the worst theory of all time yet nonetheless continue to hold onto its facthood status?

The answer is that evolution is deemed a fact because evolutionists know the world could not have been intelligently designed. The world’s evil, inefficiency and inelegance all mandate a thoughtless creative force. Like a fancy sports car with its steering wheel on backwards, this world doesn’t make sense. No designer capable of creating this world would have intended for it in the first place.

But of course intent is not a scientific quantity. The evolutionary mandate derives from secret knowledge, not public knowledge. Its foundation is gnosis, not scientia.

And so how well evolution fares in light of empirical science matters very little. That is a topic for research. It falls in the category of how evolution occurred, not if evolution occurred. No amount of empirical, public, evidence can change the private fact of evolution. Gnosis trumps scientia every time.

All of this means that one cannot argue with evolutionists from the scientific evidence. What a designer would and would not have intended cannot be learned from a scientific experiment. It does not derive from empirical findings. Rather, evolution is mandated by personal, religious beliefs that are not open to debate. Evolutionists accuse their skeptics of religious bias when they themselves are the ones who infected science with a metaphysical Trojan horse.

All of this means that evolutionary predictions and their falsifications mean very little. If a prediction or a test, such as Darwin’s proposal above, turns out to be false, it simply means that the test was ill conceived. Perhaps evolution needs to be modified, but it cannot be refuted.

As Lakatos explained, the sub hypotheses can be forfeited. They are the protective belt shielding the theoretical core. Evolution’s theoretical core is creation by natural means. The particular details don’t so much matter. Selection can be replaced by drift, gradualism can be replaced by saltationism, random mutation can be replaced by pre programmed adaptation, the evolutionary tree can be replaced by a web, even common descent can be replaced. But naturalism cannot be replaced.

So when a prediction goes bad, it is the fault of the sub hypothesis, not the theoretical core. Naturalism can never be questioned, regardless of the evidence. A good example of this came in a paper by evolutionist David Penny published last month in which Penny explained how we should understand the failure of a prediction he used to uphold evolution thirty years ago.

As I have explained, evolution predicts that different traits point to the same tree. Various evolutionary effects may cause occasional differences between the trees, but roughly speaking, if different traits are used to reconstruct the evolutionary tree, they should produce similar trees.

Thirty years ago Penny attempted to use this prediction to make evolution truly testable. In a paper published in the world’s leading science journal, Penny argued that dissimilar trees would “refute the existence of an evolutionary tree”:

Our strategy is to take different protein sequences for a common set of taxa, find all the minimal (and near minimal) evolutionary trees and then compare them. Should the probability be high that these trees are unrelated, this would indicate that the protein sequences do not contain similar evolutionary information, and hence would contradict the existence of an evolutionary tree for those taxa.

Penny used five proteins (cytochrome C, hemoglobin A, hemoglobin B, fibrinopeptide A and fibrinopeptide B) to infer the evolutionary relationships between eleven different species (rhesus monkey, sheep, horse, kangaroo, mouse, rabbit, dog, pig, human, cow, and ape). There are millions of different ways that eleven species can be arranged in an evolutionary tree. Penny used the protein comparisons between the different species to judge which of the arrangements would be more likely if they indeed were related via evolution. Penny repeated this process five times, once for each protein, and he obtained similar results. That is, the most likely evolutionary trees suggested by the five different proteins were all similar (actually there were significant differences, but as usual the test was against purely random trees). Penny concluded that “the existence of an evolutionary tree for these taxa is a falsifiable hypothesis.”

Today, thirty years later, things have changed. We now have orders of magnitude more sequence data and Penny’s prediction has been falsified many times over. There are plenty of protein and DNA sequences that do not agree, but produce incongruent evolutionary trees.

So did evolutionists reevaluate their beliefs? Did Penny conclude there is no evolutionary tree? Of course not. As Penny now writes in his new paper, he is “not rejecting the tree per se but enriching the tree concept into a network.” The new answer is horizontal gene transfer, which evolution is supposed to have created against all odds so that evolution could happen.

Evolution’s falsified predictions—and there are many, most of evolution’s predictions have turned out false—do not matter. For none of this changes the evolutionist’s certainty that the alternatives are wrong. In other words, evidence against evolution does not remedy the problems with the design hypothesis. The intent problem is no less a problem simply because biology doesn’t support evolution. Perhaps we can’t figure out how the sports car came to be, but it still has its backwards steering wheel. It must not have been intended that way.

Wednesday, July 27, 2011

You never tire of telling the world that science is driven by religion, and, in some cases there is some truth to that.

Yes, there are several arguments for the fact of evolution. They all entail theological claims (or philosophical claims which ultimately trace back to theological claims) about god.

But it is also true that your continuing rejection of common descent in the face of massive amounts of evidence reveals that you are driven by religion just as much as anyone else.

From a scientific perspective common descent is unlikely. It is true there is evidence for common descent, just as there is plenty of evidence for a flat earth, geocentrism, etc.

My question is, what is your religion?

I am a Christian, which unlike many religions, affords me a wide spectrum of explanations for origins, ranging from secondary (natural) to primary (miracle) causes.

Or, more to the point, exactly what doctrine of your religion is it that drives your deep visceral contempt for evolution …?

There is a long history of empiricism in Christian thought. Rather than imposing a framework or answer on science a priori regardless of which way the evidence points, as evolutionists do, I believe in allowing the evidence to speak for itself.

I’m not saying rationalism has no place or that blindly following the evidence solves all problems. I would agree there is, necessarily, a mix. Nor am I saying that rationalism, itself, is fallacious.

But extreme rationalism, and evolution is a good example of this, is susceptible to confirmation bias and misrepresentation of the empirical evidence. Never let an extreme rationalist represent empirical science. That would be like having a Republican speak for President Obama.

From an empirical science perspective, evolution’s failure is truly epic. There are 27 orders of magnitude between evolution’s expectations and reality. And that is going by the evolutionist’s own reckoning (in reality it is 100+ orders of magnitude). No theory in the history of science comes anywhere close to this epic failure. It is another creation myth that over and over is scientifically ridiculous.

I much prefer empiricism to mythology.

From a religious perspective I can take evolution or leave it. It doesn’t matter to me if the earth is old or young, if God used primary or secondary causes, and so forth. But by the same token, I am against superimposing a religious framework on the evidence as evolution does, and force fitting the evidence into that framework when otherwise it obviously doesn’t fit.

Tuesday, July 26, 2011

Charles Darwin’s theory of evolution states that the species arose from earlier species. Slight changes accumulating over long time periods resulted in one species giving rise to a new species, over and over.

Prediction

In this evolutionary process new species sometimes branch off from older ones and the history of life forms a tree-like pattern—an evolutionary tree. Indeed, the one figure in Darwin’s book, shown below, was that of such a pattern.

As evolutionists further elaborated on Darwin’s idea in the twentieth century the concept of an evolutionary tree became increasingly foundational to the theory. This figure below from a leading textbook [George Johnson, Jonathan Losos, The Living World, Fifth Edition, McGraw Hill, 2008.] is typical.

As the textbook explains:

Today scientists can decipher each of all the thousands of genes (the genome) of an organism. By comparing genomes of different organisms, researchers can literally reconstruct the tree of life. The organisms at the base of the tree are more ancient life-forms, having evolved earlier in the history of life on earth. The higher branches indicate other organisms that evolved later.

Evolutionists have even developed a Tree of Life Web Project, shown below, that provides information for each species and how the different species are related in the evolutionary tree:

And as more genome data have become increasingly available evolutionists naturally assumed it would be feasible to derive a comprehensive evolutionary tree:

Once universal characters were available for all organisms, the Darwinian vision of a universal representation of all life and its evolutionary history suddenly became a realistic possibility. Increasing reference was made to this universal, molecule-based phylogeny as the “comprehensive” tree of the “entire spectrum of life” [13, 14, 15, 16, 17].

A key corollary of this evolutionary tree concept is that the different traits of the species agree and point to the same tree. Various evolutionary effects may cause occasional differences between the trees, but roughly speaking, if different traits are used to reconstruct the evolutionary tree, they should produce similar trees. There may be some evolutionary “noise,” but different traits should mostly agree.

In the early twentieth century blood immunity studies provided just such confirmation. The results provided a new trait that could be used to judge the similarity and difference between different species. When the results were found to agree with the previously established evolutionary tree based on visible traits, evolutionists hailed the findings as new proofs of evolution.

Similarly, evolutionists hailed similar confirmations in the molecular sequence data that were discovered later in the century. Here is evolutionist Jerry Coyne’s summary from his recent book Why Evolution Is True:

Creatures with recent common ancestors share many traits, while those whose common ancestors lay in the distant past are more dissimilar. The “natural” classification is itself strong evidence for evolution. [p. 9]

Strong evidence indeed. Evolutionist David Penny made the point that this evidence provides a means to falsify evolution. The philosopher Karl Popper had argued evolution is not falsifiable, but for Penny this evidence proved Popper wrong. Penny showed how different proteins, compared across different species, lead to similar evolutionary trees. If they hadn’t, Penny argued, evolution would be false.

Falsification

Now, thirty years after Penny cited the congruence of different evolutionary trees as a prediction that could falsify evolution, it is not controversial even amongst evolutionists that the prediction is false. The plethora of new DNA and protein sequence data have provided a steady stream of incongruent evolutionary trees. These trees strongly conflict with the trees based on other sequence data, or with the consensus evolutionary tree. And the disagreement is far beyond evolutionary “noise.” As one evolution wrote:

Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.

Another paper admits that “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”

Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.

Evolutionists are not sure just what the data mean, but even they agree that different traits, across different species, often do not produce congruent evolutionary trees. And the difference is not mere “noise.”

Reaction

How do evolutionists deal with this falsification? David Penny, the evolutionist who cited the congruence of different evolutionary trees as a prediction that could falsify evolution now has a different story. Penny now reveals that congruent trees never really were a prediction of evolution. After all, Darwin was not nearly so keen on promoting the evolutionary tree concept as he was descent with modification. In fact, according to Penny, the new evidence “enriches our understanding of evolution.”

Likewise, another paper argues that perhaps the evolutionary tree was more of a heuristic than a prediction.

And as usual evolutionists appeal to a spectrum of explanatory devices to correct the narrative. The most prevalent of these epicycles is the horizontal gene transfer (HGT), a term that encompasses several known mechanisms by which genes can transfer between organisms such as bacteria.

In fact, if evolution is true then HGT must have been one of its key players. As one paper explained, HGT “has emerged as a central force in the evolution of many different prokaryotes.”

and now cases of HGT in eukaryotes are emerging at an increasing rate and account for many adaptively important traits

So HGT is now a key mechanism of the evolutionary process. It can do what the old mechanisms could not. In fact, one must wonder how this powerful mechanism knows when to send which genes where. For the various versions of HGT are incredibly intelligent.

For instance, consider the HGT process of transformation in which DNA from the extracellular environment is imported into the cell via what one paper describes as “a complex process” involving a small army of protein machines.

Then there is the HGT process of conjugation in which the DNA is transferred via cell-to-cell contact. A bridge-like connection is constructed between the two cells through which helpful DNA is transferred. And the donor cell has the molecular machinery to verify that the receiving cell does not already possess the donated DNA. And the DNA includes genes critical in the conjugation process. The DNA to be sent over is nicked and unwound so a single strand can be threaded through the bridge connection.

Serendipity squared

Gone are the days of simple mutations creating so much of the biological world. They were reminiscent of those swerving atoms of the Epicureans. And like those swerving atoms, they are prima facie incapable of creating biology’s wonders.

Beyond this obvious failure, much more than mutations are required to explain biology’s patterns. The evolutionary tree is out and networks, or webs, or some such, are in. And a new set of mechanisms, such as HGTs, are the brains behind the creation.

But epicycles are not free. In this case, the marshalling of HGTs as the explanation for biology’s patterns and success raises the question of where these complex mechanisms came from in the first place. According to evolutionary theory, evolution created the incredibly complex HGTs which then facilitated, yes, evolution.

Do they seriously expect us to believe this? Religion drives science, and it matters.

Saturday, July 23, 2011

One of the fundamental predictions of evolution is that life must have had simple beginnings. Life is complex and ever since Darwin evolutionists have tried to explain how that complexity arose over time, for life must have had simple beginnings. An obvious problem here is that even the fundamental unit of life—the cell—is itself profoundly complex. And this problem has not been aided by evolutionist’s attempts to reconstruct what that first cell might have looked like. The results were confusing due to the wide variety of genes between and amongst life’s three lineages. No clear picture of a simple progenitor emerged. Instead, the only solution seemed to be a super progenitor that already had most of the highly complex traits found in each of the three lineages. The super progenitor would have been as complex as modern cells yet would have somehow arisen in a short time. It seems that first born cell of evolution must have been quite complex, including a vast proteome of hundreds of different proteins. This is just one of many scientific falsifications of evolution’s prediction of simple beginnings.

Simple cells like bacteria are supposed to be, well, simple. They might have transformed Earth because of their unimaginable numbers, but they’re little more than tiny, solitary bags of chemicals. Or so we thought. Here, New Scientist looks at the growing number of exceptions to the rules. The most recent discoveries are challenging our ideas about the nature of early life.

Their examples are interesting but hardly new. The problem of early complexity could have been explored a decade ago or a century ago. It is yet another in a long list of evolutionary expectations that is contradicted by science. Religion drives science and it matters.

Friday, July 22, 2011

In statistical testing there are Type I and Type II errors where the null hypothesis is erroneously rejected and erroneously accepted, respectively. In simple terms we might call these false alarms and missed alarms. Likewise as evolutionists rack up their false conclusions they commit both of these two types of errors. On the one hand, they erroneously conclude the evidence supports evolution. On the other hand, they just as commonly fail to see the many failures of their theory. A good example of this is in a paper published in the leading journal Nature on protein evolution which I discussed in my previous post.Type I errors

The paper uses a somewhat circuitous method to conclude not only that protein evolution is continuing but that their analysis provides yet more “novel evidence of the common ancestry of life.”

But evolutionary assumptions slip into their analysis at several entry points. The evolutionists beg the question when they conclude their results are evidence for evolution and common descent. In fact their findings support no such conclusion. It is a Type I error typical of the evolution genre.Type II errors

What is perhaps more interesting are the many Type II errors which one must read between the lines to see. For instance, if proteins ever were actually to evolve it would require a long time (far longer than the age of the universe, for example). The paper does nothing to remedy this problem, and in fact agrees that protein evolution is not a hasty affair.

But the evolutionist’s research takes as its starting point a vast population of proteins, which they suppose to be present in the early earth environment, a good three and a half billion years ago.

But from where did all these complex and advanced proteins come and how did they arise so rapidly so as to be ready and waiting for evolution to use them? This is, of course, absurd. It is a monumental Type II error which evolutionists conveniently ignore.

Another major problem for protein evolution, which the paper amplifies, is that proteins are hard to find. As stated above, their evolution would require a long time. This is because the fitness landscape between them is rugged, and there generally is no gradually increasing slope leading to nature’s thousands of different proteins.

Again, the paper does nothing to remedy this situation. And in fact, by way of rationalizing its results, the paper further aggravates the problem. Because the paper finds that the supposed evolution of proteins must have been rather slow, the evolutionist’s imagine that a process known as epistasis retarded the process. The idea is that mutations, and the resulting changes to the protein’s amino acid sequence, impact the other amino acids in the sequence. So whereas a particular amino acid might have been useful or not useful before a mutation occurs, all that may change after the mutation. The upshot is that the protein evolves by following a circuitous, maze-like path through evolutionary history.

What is important, and unspoken, about this idea is that it calls for the mother of all serendipities. Consider this. Certain types of amino acid changes must occur for a protein to evolve into another protein. At the start, these amino acid changes cannot occur because they are harmful. It appears that protein evolution just isn’t going to happen.

But, as evolutionists argue, the few amino acid changes that are allowed at the beginning act to change the usefulness of other key amino acids, so they can evolve in the right way. Those changes then, in turn, act on yet a few other amino acids to change in the right way. The process continues and so the dominoes fall in just the right way, luckily ending at a new, useful, protein that otherwise was impossible for evolution to find.

It is yet another ludicrous appeal to the astronomical serendipity that silently undergirds much of evolutionary theory. And it is another Type II error.

These are not the only Type II errors in the paper. Evolutionary theory routinely must turn a blind eye to the plethora of contradictions in the data. Religion drives science, and it matters.

Tuesday, July 19, 2011

In my previous post I discussed a paper published in the leading journal Nature on protein evolution. In spite of the scientific evidence showing the evolution of proteins is unlikely, the paper finds that proteins are indeed excellent examples of evolution—past, present and future. For instance, the evolutionists write:

Figure 3 shows that, regardless of their similarity, ancient proteins are still diverging from each other and therefore have not yet reached the limit of their sequence divergence. … Our data reveal an ongoing expansion of the protein universe, such that most extant protein sequences are still diverging from each other and from the ancestral LUCA sequence, and have not yet reached the structural and functional limits in sequence space.

But in fact their results show no such thing. Indeed, that would be quite amazing given that science clearly shows protein evolution to be unlikely. It would be the reversal of a wealth of evidence. What they do show is the results of a circuitous analysis and comparison of many different proteins. It would require substantial scientific investigation to come to any firm conclusions about just what those comparisons portend.

What is obvious is that the evolutionists, in typical fashion, have presented a bizarre and heroic conclusion that is without scientific basis. There is nothing in the data about “ancient proteins” that are “still diverging” from an “ancestral LUCA.” Once again, the results are force fitted into the evolutionary narrative, over against scientific evidence and without warrant.Evolutionists drink their own bathwater

In spite of its scientific problems, this paper is being cited by other evolutionists as an authoritative finding and confirmation of protein evolution. For example, one evolutionist, referring to this paper wrote “The protein universe is currently still expanding …”

In another instance, evolutionists wrote that their research “is entirely in accord with a recent insightful analysis of protein evolution that invoked extensive epistasis to account for the retarded divergence seen in ancient proteins.”

Call it garbage-in, garbage-out, or blowback, or drinking their own bathwater, this is how evolutionary claims propagate. It begins with religious and metaphysical claims for evolution. From there science is enlisted to service the religion. Empirical evidence is twisted and force-fit as necessary, and then cited uncritically as though it is legitimate science.

The duty of a scientist

All of this is a serious breach of scientific duty. For scientists must practice their profession with integrity and, above all, interpret and explain the evidence accurately to the rest of society. Unfortunately evolutionists not only promote a religious theory, they also misrepresent the many scientific failures of the theory. In fact, incredibly, they maintain there are no scientific problems with theory. All of the science, they insist, confirms their bizarre idea, with only the details left to be figured out.

Even this paper on protein evolution is staunchly defended as yet another scientific confirmation of evolution. One professor commented that the paper has a sound basis and that my review of the paper was due to my “profound misunderstanding of the article.” Regarding my point, that for two distant proteins, an amino acid is not likely to change the distance between them, the professor wrote:

It is well known that a single random walker moves away from the point of origin, on average: the distance squared is proportional to the number of steps taken. The same is true for two random walkers: the square of the distance between them grows, on average, no matter what the initial distance was.

This is true for random walkers in Euclidean space, and is typically taught in introductory material. This is probably what the professor was thinking of. But of course protein sequence space is non Euclidean. Amino acids are categorical and unordered. The professor continued:

Cornelius seems to think that closely related proteins should diverge fast and more distant relatives less so.

I think that because it is rather obvious, as I pointed out with some simple examples.

What Cornelius forgets is that we are dealing not with two proteins but with many. Suppose that the proteins have been mutating for a long time and have uniformly filled the configuration space. (For simplicity, think that there is one protein in every configuration.) … This factor, missing from Cornelius's analysis, makes the observed numbers of proteins mutating to and away from a reference equal.

Here the professor raises a meaningless distinction. First, while problems with one or two or three dimensions are common, protein sequence spaces are in the hundreds of dimensions. It would be impossible to have enough different species to have a protein in every configuration. For instance, for a 200 amino acid protein there are 10^260 different possible sequences (a one with 260 zeros after it).

But beyond that, the professor thinks that the effect of a substitution on the distance between two protein sequences is independent of the distance. Specifically, he thinks the substitution has an equal chance of moving toward or away from a reference sequence. But he gets his math all wrong trying to arrive at this impossible conclusion. Let’s have a look at his example.

Consider the five residue reference sequence: NLKIG. There are a total of 5*19 or 95 sequences that have only one amino acid different from the reference. So these 95 sequences completely fill the sequence space at this given distance from our five residue reference sequence.

Now for each of these neighboring sequences, consider a single amino acid substitution. There are 19 such substitutions possible per residue. So the number of possible substitutions, in each of the 95 sequences, is also 5*19 or 95.

Now of these 95 substitutions, exactly one of them changes the neighboring sequence toward the reference sequence. 18 of them change the neighboring sequence into a different neighboring sequence. And 4*19 or 76 move the neighboring sequence away from the reference sequence.

You can repeat these computations for the other 94 neighboring sequences, but of course the answers are the same. It makes no difference whether you look at one neighboring sequence or all 95 of them. The probability of a substitutions moving toward the reference sequence is 1/95 whereas the probability of a substitutions moving away the reference sequence is 76/95.

The professor continues with an analogy about people randomly walking about an island:

At any given moment, a friend's step can be toward or away from you with equal probabilities

That is false. In two dimensions it is close to equal, but with more dimensions the disparity increases. Nonetheless the professor concludes:

In equilibrium, the outward and inward fluxes are the same at any radius. This is a key idea behind the work of Povolotskaya and Kondrashov. Cornelius completely missed it.

Again this is false. It doesn’t matter how long sequences have been changing, or how full the sequence space is. The paper provides results which no doubt mean something, but a confirmation of evolution they are not.

How can evolutionists so consistently misinterpret science so badly? There is no mystery here. Evolutionists must have their theory so they will do whatever is necessary to force-fit the science to support it. Religion drives science and it matters.

Addendum

We are now entering the irrational stage of the discussion. When evolutionists are confronted with their logical fallacies, metaphysical mandates or misrepresentations of science, the discussion inevitably does not end well.

In this case, the professor now says that his concerns have dealt with the academic problem of infinitesimal steps in his random walk. That’s strange, I thought he was discussing an example of people walking around on an island. That is a real-world problem with finite, not infinitesimal, step sizes.

This is important because the problem at hand, amino acid substitutions in proteins, also deals with finite step sizes (not to mention categorical and unordered variables). So now the professor can claim victory for an irrelevant problem.

Friday, July 15, 2011

In my previous post I discussed a paper published in the leading journal Nature on protein evolution. In spite of the scientific evidence showing the evolution of proteins is unlikely, this paper is used as an apologetic by evolutionists for why said evolution is actually no big problem. The paper uses a somewhat circuitous method to arrive at its conclusion that protein evolution occurs early and often and that the findings are yet more “novel evidence of the common ancestry of life.” These conclusions are false and are based on a naïve and circular analysis. This is not easy to understand, however, because the analysis is circuitous. Here I will provide a simple explanation to help illustrate the fallacy.

Case 1: Two proteins that are different

Consider two proteins whose amino acid sequences are very different. You align and compare the sequences and find that fewer than 10% of their amino acids are identical. This is about what would be expected from two random sequences and we say that the distance between the proteins is large.

Now imagine that a mutation occurs, changing one of the amino acids in one of the proteins. Most likely the distance between the proteins remains unchanged. For instance, let’s say the amino acid mutated from alanine to valine. Meanwhile, the corresponding amino acid in the other protein is proline. So both before and after the mutation, the amino acids in the two proteins do not match, and the distance between the proteins remains unchanged.

There is a slight chance that the mutation could produce a match. The alanine could mutate to a proline. On the other hand, there is a slight chance that the mutation could eliminate a match. This would be the case if the original amino acid had been a proline. So there is a slight chance the mutation could either decrease or increase the distance. But these to events are unlikely, and in any case they average out. The bottom line is that for two distant proteins, a mutation is not likely to change the distance between them.

Case 2: Two proteins that are similar

Next consider two proteins whose amino acid sequences are very similar. Instead of 10%, let’say 90% of their amino acids are identical. In this case the distance between the proteins is small.

This time, a mutation most likely would increase the distance between the two proteins. This is because the mutation will probably change an amino acid that previously had matched the corresponding amino acid in the other protein. For instance, if corresponding amino acids in the two proteins are both alanine, and the mutation causes one of them to switch to valine, then the match is destroyed.

There is a slight chance that the mutation could produce no change to the distance, or even decrease the distance by producing a match, but in most cases the mutation increases the distance.Conclusion: A mutation’s effect on distance depends on the distance itself

So the conclusion is that a mutation’s effect on distance depends on the distance itself. Specifically, for distant proteins, a mutation has little effect on distance. But for similar proteins, mutations usually increase distance.

This simple fact was a key result of the paper. In their research, the evolutionists performed a lengthy and circuitous analysis which demonstrated this straightforward relationship. It would be like a Rube Goldberg device that prints out: A = A.

Here is the figure in the paper showing the relationship. The average effect of mutations on the distance between the two proteins is plotted on the vertical axis. A small value close to zero means mutations will increase the distance. A value of one means that overall the mutations do not change the distance. These data are graphed versus the distance between the two proteins on the horizontal axis. As the solid line indicates, at short distances mutations will increase the distance. And at long distances mutations will not change the distance.

It may seem amazing that a leading journal would accept such meaningless research, but this is not too unusual for evolutionary papers. Starting with the “evolution is true” premise tends to blind one to objective analysis. And this is true for reviewers as well as authors.

This is a case where the classic criticism “it isn’t even wrong” applies. Researchers can make mistakes and an otherwise fruitful approach can produce erroneous results. But here there is no computational or scientific mistake. The evolutionists haven’t blundered. Rather, qua evolutionists they have followed their instincts and interpreted a meaningless tautology as powerful evidence for evolution. And of course evolutionists have welcomed it with open arms. The entire approach is absurd, but evolutionists are blind to their abuse of science.

Wednesday, July 13, 2011

In spite of common sense and the scientific evidence, evolutionists have once again shown that evolution is a miracle worker. A new paper by evolutionists in the world’s leading journal argues that proteins evolved after all, despite just about every shred of evidence mandating otherwise. And just how did evolution do it again? It turns out proteins evolved because they evolved. If only I had thought of that—I could be an evolutionist too.

Not even wrong

The new paper acknowledges that molecular reality “severely restricts” the mutational changes a protein can undergo. Indeed, “the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape” make all but about 2% of the possible mutational changes unacceptable.

But since we know evolution is a fact, then proteins too must have evolved. One is tempted to say the research is wrong, but that would be a compliment. For it isn’t even wrong—it is downright ridiculous.

The fact that it found its way into the world’s leading scientific journal is a testament to how badly evolution has infected science. In the paper (details below), the evolutionists conclude that similar proteins are evolving away from each other faster than distant proteins are evolving away from each other. Just like Hubble’s receding galaxies right? Wrong. Once again evolutionists make a flawed analogy with physics, but that’s another story.

With their circular findings in hand, the evolutionists leap to a series of equally circular conclusions: (i) Rest assured, proteins are still busy evolving though sequence space for evolution has not reached its limit, (ii) All that evidence against protein evolution must be misleading, (iii) Proteins must be evolvable by the magic of epistasis, and (iv) The results are yet more evidence for evolution.

And you thought epistasis was a problem for protein evolution. After all, it makes for a rugged fitness landscape in the protein sequence space, greatly complicating any evolutionary search. Silly you—the evolutionists have turned it into a virtue. Yes it may appear that proteins cannot tolerate much change, but what if that tolerance is ever-changing in just the right way due to epistatic effects? Then the tiny amounts of tolerable change could be, themselves, ever changing. And so evolution can magically find a maze-like path to another protein. Just when you thought you had seen peak fallacy, the evolutionary speculation reaches new heights.

A self-refuting theory

And as usual, what little legitimate science there is in the paper easily refutes the very idea the evolutionists purport to confirm. What the evolutionists get right is that if evolution were true then protein evolution would take a long, long time. What they don’t get around to thinking about is that this undermines their silly thought experiment, which begins 3.5 billion years ago with all manner of proteins already fully formed. That leaves only a few million years for their origin, which isn’t enough time to create them from a warm little pond.The details

For those who like to waste time probing junk science, here is an explanation of the evolutionary folly in this paper. The evolutionists begin by assuming evolution happened. Not a good start if you want to prove evolution. But moving beyond the usual petitio principii, they next compare similar proteins and find what they think is a curious pattern.

Imagine, for example, three proteins with very similar sequences. These are illustrated below as Proteins 1, 2 and 3. Next, imagine a fourth protein that is a bit more different. If the first three proteins are siblings, the fourth is a cousin.

Now in the first three protein sequences, there are very few differences. One difference highlighted in the notional example below at the third position is the tyrosine amino acid (Y) in Protein 1. It is different from the lysine (K) in Proteins 2 and 3.

But note that Protein 1’s tyrosine is also different from Protein 4, which also has a lysine at the third residue position. When one of the first three proteins differs from the other two, it will likely differ from Protein 4 as well because Protein 4 is fairly similar.

Now consider a second example illustrated below. In this case, Protein 4 is more distantly related. It shares fewer sequence matches with the first three proteins. Because Protein 4 is more distant, differences among the first three proteins, by definition, are less likely to differ from the Protein 4 sequence.

Or in other words, there is a better chance that a difference in one of the first three proteins might actually match the corresponding Protein 4 amino acid. This is illustrated below, as Protein 1’s tyrosine now matches the tyrosine in Protein 4. That would be much more unlikely if Protein 4 was more similar, as in the first example above.

There is nothing clever or profound here. As Protein 4 becomes increasing distant from the first three proteins, it simply follows that differences among the first three might not differ from the fourth sequence.

This simplified explanation is not what the evolutionists did, but it gives a rough idea of the circuitous calculations the evolutionists used to try to confirm evolution. In the end, all they did was to prove a tautology. Below is their “key” result. The straight line illustrates the strong relationship between the distance between proteins and how the differences compare.

Only evolutionists could find this to be significant. As the graph not surprisingly shows, at short distances the differences in the protein sequences are more likely to show (as in the first example above). At greater distances, the differences are less likely to show (as in the second example above).

And given the degree of these differences, something must be slowing evolutionary progress. It must be epistatic effects which the evolutionists then enlist to contrive another one of evolution’s heroic just-so stories. In this case, the epistatic effects change as mutations accumulate so that mutations that once were not tolerable are now tolerable. And amazingly, these epistatic pathways just happen to lead to functional proteins that otherwise are so difficult to find in the protein sequence space.

If you don’t follow all this don’t worry. It is a silly, convoluted tautology that has no place in a scientific journal. Like a Rube Goldberg device that spits out A = A, the research is much ado about nothing.

And yet this is touted as new, novel evidence for protein evolution and common descent. As the evolutionists conclude:

Finally, our observation of receding protein sequences provides novel evidence of the common ancestry of life.

What an astonishing abuse of science. Yet here is how one professor responded to an earlier post of mine regarding protein evolution and this paper:

It's telling that he relies [especially in his point 4: Experiments show that proteins do not tolerate mutations very well] on his misunderstanding of a paper that he has cited repeatedly:

Would that I were the problem. Unfortunately evolutionary science—surely an oxymoron if there ever was one—is idiotic. To the uninitiated that may sound like hyperbole but it’s not. When something—like the idea that the universe and everything in it just happened to arise spontaneously—is idiotic, the best word to describe it is “idiotic.”

But when you point out the fallacies the evolutionists blame you. After all, evolution is a fact. Religion drives science and it matters.

The leading evolutionist of the twentieth century, Ernst Mayr, once wrote that evolution achieved its predominance “less by the amount of irrefutable proofs it has been able to present than by the default of all the opposing theories.” Or as Stephen Gould put it:

Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.

Indeed, evolution’s proof texts are always religious.

I’m not sure which is more disgusting, evolution’s hypocrisy or its self-promotion. Evolutionists proclaim their religious lies and hypocrisy as though the world will be impressed. And we hear it again and again.

I recently mentioned a protein named p53 that is yet another example of how science contradicts evolution. An evolutionist responded with the usual phony scientific arguments:

Well, one could predict that if TP53 is involved in so many systems / pathways that are fundamental to a host of cellular processes including (but probably not limited to) cell cycle regulation, apoptosis and senesence, then it had to have originated around the time that the simplest forms of multi-cellular life emerged and therefore would be present in the simplest of life forms as well as the most complex. One could also predict that the separate genetic changes that may have affected this gene as different lineages diversified would allow scientists to generate some sort of phylogeny maybe? Perhaps, TP53 may even be part of a larger 'super-family' of genes that have homologs and orthologs throughout multi-cellular life forms that also, through genetic analyses, appear to form some sort of hierarchy... If only scientists could find such a thing huh.

Oh yeah, the p53/p63/p73 superfamily. Highly conserved genes found all the way up from C.elegans to H.sapiens.

http://cshperspectives.cshlp.org/content/2/7/a001131.full

I'd post more links but don't see the point. The info is out there for those who wish to see it. No amount of linking to primary data or peer-reviewed journal articles will help those that don't want to.

CH, p53 is not a good example if you want to poke a stick at the ToE.

When I explained the scientific problems he responded with the usual religion:

Problem I have Mr. H is that even if I were to accept your points I still can't think of any credible alternative. The OT/genesis/creation is obviously a fairytale, or at best an allegory. I don't see how ID is anything other than a kind of anthropomorphic projection that will probably be as guilty of everything you claim is wrong with ToE.

In other words, scientific problems don’t count. Evolutionists are religious fundamentalists who must have evolution. They bring their religion into science and their religion requires a naturalistic creation story, regardless of how absurd. So they will spin whatever scientific-sounding arguments they can to prop up evolution.

Evolution is a religious Trojan Horse that has penetrated science and gone viral. Evolutionists have entered science though a different door. They abuse science, manipulating and perverting the obvious evidence as the need arises.

Tuesday, July 12, 2011

Evolutionists say they just don’t know how to discern miracles. They might begin by looking at a protein. Proteins, according to science, are not likely to have evolved. And when I say “not likely,” I mean the chances are astronomically against such evolution. I may as well simply say: Proteins, according to science, did not evolve. To review, very briefly, here are some of the reasons:

1. Not enough time. New genes are found in species which allow only for a few million years for protein evolution.

2. Too important. These new genes are not functionally less important, as they should be if they recently evolved.

4. Inflexible. Experiments show that proteins do not tolerate mutations very well. They rapidly lose their function with only a few mutations, so the evidence indicates that to evolve to a protein you need to start very close to it.

5. Not searchable. The protein design space is astronomically large and experiments show it provides no guidance as to where the fully functioning proteins are in the space. Like looking for a needle in a haystack, the hay provides no guidance.

I have discussed this issues here, here, here, here and here. Now if you already believe evolution is true and you don’t mind ignoring the obvious scientific evidence and you don’t restrict yourself to plausible explanations then, yes, you can explain all of the many issues with protein evolution using a variety of non scientific, just-so stories.

But for those who respect science, the evidence we currently have is clear. In fact, unlike most of the evolution narrative which appeals to a great many contingencies over a great many years in the past, protein evolution is more amenable to scientific experimentation. The just-so stories give way to the raw data of experiments which, not surprisingly, clearly show protein evolution to be unlikely.

Of course evolutionists attempt to spin the results of these experiments to favor their theory. They ignore monumental assumptions and use calculations that unrealistically favor evolution. But even then—even giving evolution every advantage—protein evolution is nonetheless unlikely.

For instance, in one case evolutionists concluded that the number of evolutionary experiments required to evolve their protein (actually it was to evolve only part of a protein and only part of its function) is 10^70 (a one with 70 zeros following it). Yet elsewhere evolutionists computed that the maximum number of evolutionary experiments possible is only 10^43. Even here, giving the evolutionists every advantage, evolution falls short by 27 orders of magnitude.

The theory, even by the evolutionist’s own reckoning, is unworkable. Evolution fails by a degree that is incomparable in science. Scientific theories often go wrong, but not by 27 orders of magnitude. And that is conservative.

How conservative? In order to educate readers about the science, as opposed to the evolution mythology, I wanted to explain not only the 27 orders of magnitude shortfall, but also why even that estimate is grossly under valued.

So I explained the several evolutionary assumptions involved. For instance, the evolutionists computed that a maximum of 10^43 evolutionary experiments are possible by assuming a time span of 4 billion years. But that is unrealistic.

Even evolutionists agree that evolutionary innovations, including proteins, arise rapidly, on the order of some tens of millions of years, or in some cases even in just a few million years. So their time span was two to three orders of magnitude too long.

In response to this, one professor made this comment:

The "evolutionist" authors to whom Dr Hunter refers (Dryden, Thomson and White, 2008), assumed a time-frame for the biological activities of bacteria on earth of four billion (4*10^9) years (a commonly accepted value).

An order of magnitude is a factor of 10, so Dr Hunter proposes that a more realistic value for the duration of existence of bacteria on earth is 100- to 1,000-fold less than 4*10^9 years, or between 4*10^7 and 4*10^6 years. That's between 40 million and 4 million years! (Faithful readers may recall Dr Hunter's previous essay on a Cambrian fossil that was dated to ~515 million years ago!)

What was he thinking?

Again, it is unrealistic to use the entire time span of bacteria on earth. Proteins must have evolved much faster than that. Indeed, the bacteria themselves are full of proteins. So giving the bacteria a four billion year time frame leaves much less time to evolve their proteins.

In another example, the evolutionists computed the maximum of 10^43 evolutionary experiments are possible by assuming a protein size of 50 amino acids. I pointed out that this is extremely small as very few proteins are this short. Indeed, the vast majority of protein domains are far longer than 50 residues. Single domain proteins, and domains in multiple-domain proteins are typically in the hundreds of residues.

In response to this, the professor made this comment:

On the contrary:

"The size of individual domains also varies widely (Fig. 6C), from 36 residues in E-selectin (lesl) (Graves et al., 1994), a two-domain protein, to 692 residues in lipoxygenase-1 (2sbl, chain B) (Boyington et al, 1993), also a two-domain protein. However, very large domains are the exception. The distribution peaks at around 100 residues per domain and 80.3% of the domains are comprised of less than 200 residues. Very similar distributions have been observed in smaller non-redundant data sets. Siddiqui and Barton (1995), using DOMAK to assign domains for a data set of 230 protein chains, found that 90% of domains comprised less that 200residues. Holm and Sander (1994) using PUU on a dataset of 330 protein chains, also observed a domain size distribution that peaked at 100 residues."

Domain assignment for protein structures using a consensus approach: Characterization and analysis

Here the professor simply reinforces my point. As the graph below shows, the protein domain sizes range from about 50 to about 700 and the majority (approximately two-thirds) are longer than 100 residues. The evolutionists used the extremely short value of 50 to try to improve their chances, but that is unrealistic.

The 27 orders of magnitude estimate, as miraculous as it is, is a ridiculously low-ball figure. The problem is so complicated we don’t have a good understanding of what the right number is, but a conservative estimate is 10^100 (100 orders of magnitude). For a typical protein of 250 amino acids, its gene has about 10^450 different possible sequences and the protein has about 10^325 different possible sequences. Thus this 10^100 estimate is an incredibly tiny fraction of the theoretical total.

What the right figure is no one knows, but the evidence we do have is clear. Protein evolution is profoundly unlikely. So why don’t evolutionists simply acknowledge this conclusion? Why don’t evolutionists go by the science? The answer, of course, is that this never was about the science in the first place. Religion drives science, and it matters.

I described here how the Human Genome project and high throughput technologies have revealed levels of complexity evolutionists hadn’t even dreamed of, revealing yet another monumental failure of evolutionary theory. One example of the discovery of new levels of complexity is the “guardian of the genome,” protein p53 which binds to thousands of DNA sites to control transcription, processes RNA, binds to proteins to modify activity, and undergoes alternative splicing to take on nine different forms:

Even for a single molecule, vast swathes of messy complexity arise. The protein p53, for example, was first discovered in 1979, and despite initially being misjudged as a cancer promoter, it soon gained notoriety as a tumour suppressor — a 'guardian of the genome' that stifles cancer growth by condemning genetically damaged cells to death. Few proteins have been studied more than p53, and it even commands its own meetings. Yet the p53 story has turned out to be immensely more complex than it seemed at first.

In 1990, several labs found that p53 binds directly to DNA to control transcription, supporting the traditional Jacob–Monod model of gene regulation. But as researchers broadened their understanding of gene regulation, they found more facets to p53. Just last year, Japanese researchers reported that p53 helps to process several varieties of small RNA that keep cell growth in check, revealing a mechanism by which the protein exerts its tumour-suppressing power.

Even before that, it was clear that p53 sat at the centre of a dynamic network of protein, chemical and genetic interactions. Researchers now know that p53 binds to thousands of sites in DNA, and some of these sites are thousands of base pairs away from any genes. It influences cell growth, death and structure and DNA repair. It also binds to numerous other proteins, which can modify its activity, and these protein–protein interactions can be tuned by the addition of chemical modifiers, such as phosphates and methyl groups. Through a process known as alternative splicing, p53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development. In fact, it seems wilfully ignorant to try to understand p53 on its own. Instead, biologists have shifted to studying the p53 network, as depicted in cartoons containing boxes, circles and arrows meant to symbolize its maze of interactions.

The p53 protein is encoded by about 1200 nucleotides in the TP53 gene which spans about 20,000 nucleotides. The 1200 nucleotides are divided amongst several exons (coding regions) which are separated by introns (non coding regions). To create p53 the cell transcribes the TP53 gene, edits the transcript, and translates the edited transcript into the corresponding sequence of about 400 amino acid according to the genetic code.

Evolutionists do not know how the highly skilled p53 protein evolved. How did one protein gain all those different functions? Evolutionists do not know. In fact they don’t know how proteins, in general, could have first evolved. Evolutionists also don’t know how genes, in general, evolved. Nor do they know how introns evolved. Nor do they know how the fantastic process of protein synthesis (gene transcription, transcript editing and translation) evolved. They don’t know how the DNA code evolved.

p53 is just one example of biology’s complexity that defies evolution. And yet this is how evolutionists typically respond:

Well, one could predict that if TP53 is involved in so many systems / pathways that are fundamental to a host of cellular processes including (but probably not limited to) cell cycle regulation, apoptosis and senesence, then it had to have originated around the time that the simplest forms of multi-cellular life emerged and therefore would be present in the simplest of life forms as well as the most complex. One could also predict that the separate genetic changes that may have affected this gene as different lineages diversified would allow scientists to generate some sort of phylogeny maybe? Perhaps, TP53 may even be part of a larger 'super-family' of genes that have homologs and orthologs throughout multi-cellular life forms that also, through genetic analyses, appear to form some sort of hierarchy... If only scientists could find such a thing huh.

Oh yeah, the p53/p63/p73 superfamily. Highly conserved genes found all the way up from C.elegans to H.sapiens.

http://cshperspectives.cshlp.org/content/2/7/a001131.full

I'd post more links but don't see the point. The info is out there for those who wish to see it. No amount of linking to primary data or peer-reviewed journal articles will help those that don't want to.

CH, p53 is not a good example if you want to poke a stick at the ToE.

In other words, if TP53 has so many fundamental functions then it must have originated early in evolutionary history. And indeed it is found everywhere from worms to humans. And if TP53 has been evolving all this time then it should roughly fit the expected evolutionary pattern. And it does. And finally, such a widespread and important gene should be part of a super family of genes. And indeed it is. So the science is obvious, isn’t it? We can acknowledge the data, or willfully ignore the obvious.

It is frightening how intelligent, knowledgeable, well-educated people can be so self assured about bad science. In fact these three predictions mentioned by the evolutionist are phony. If genes did not appear in super families evolution would be perfectly happy. Likewise, if genes fell into unexpected, contradictory patterns it would pose no problem. And if TP53 was not ubiquitous evolution would be unharmed.

How do I know this? Because it happens all the time. These predictions are more like Lakatos’ auxiliary hypotheses. Convenient explanations of the data that are gratuitous and may be forfeited. They are the protective belt that shield the theoretical core. Serviceable as “proofs” when correct, the stuff of good solid scientific research when incorrect.

This response above is typical. These soft “predictions” are touted as no-brainer, compelling proof-texts of evolution. But in fact these “predictions” are repeatedly falsified.

And even if they were true the reasoning amounts to the fallacy of affirming the consequent. Geocentrism isn’t true because the sun traveled across the sky today.

What is perhaps most astonishing, however, is the steadfast faith of evolutionists in the face of utter failure. Forget about evolution’s soft “predictions” that are consistently wrong, or the evolutionist’s faulty logic. Those breakdowns are minor compared to evolution’s inability to provide anything beyond sheer speculation on just how life is supposed to have arisen by itself.

As stated above, the Human Genome project and high throughput technologies revealed levels of complexity evolutionists hadn’t even dreamed of. Not that this was new news—even in Darwin’s day it was clear biology was fantastically complex. Darwin provided no plausible rationale for its evolution, and nothing has changed since 1859.

Evolution is an utterly ridiculous, religiously-motivated notion that has no scientific standing. This is not hyperbole but rather a simple description of the facts. Religious proofs underwrite the theory in spite of the obvious scientific evidence. Evolution is not a minor error. It is not a theory that merely needs some tweaks and adjustments. It is an absurdity that is obvious to anyone with common sense. Religion drives science and it matters.

Monday, July 11, 2011

Evolutionists say they cannot reckon with miracles. They don’t know how to determine if naturalistic explanations don’t work. Therefore science must be limited to naturalism and, indeed, anything else is a science stopper according to evolutionists.

But the fact that evolutionary science can only reckon with naturalistic explanations does not mean that only those explanations are true. This would be like an automobile mechanic claiming that jet aircraft cannot be real because, after all, he does not possess the knowledge or tools to work on them. Evolutionists say they lack the tools to test and evaluate theories that are not strictly naturalistic, but this does not mean such theories are necessarily false.

The irony here is that evolutionists make naturalism unscientific according to their own criterion of testability. This is because naturalistic explanations are the only explanations that are allowed. Imagine if the species were designed. What if the DNA code, the bat’s sonar system and the many other biological wonders were created by a miracle. If this were true, it would not be allowed within evolutionary science. Evolutionists would forever be trying to figure out how such marvels evolved. And they would continue to insist that evolution is a fact.

Of course evolutionists are not fooling anyone but themselves. When you hear an evolutionist claim that evolution is a fact you know there is an commitment to naturalism underwriting the claim.

Digging holes

But it doesn’t help to point out these problems to evolutionists, as I did here and here. They just dig themselves in deeper and deeper. One evolutionist in the know made this comment:

In simple language, that is not my view. Evolutionists make metaphysical arguments for why evolution is a fact, and when you point out their logical fallacies and scientific errors they blame you for introducing the metaphysics. It seems the evolutionist always blames you for what they do.

In fact I discussed two legitimate ways evolutionists can do science without sacrificing their commitment to naturalism. But as usual, the evolutionist rejects them for they strip away his metaphysics. It’s no fun following the rules if you can’t have your way. The evolutionist continues:

Oh, and please give us some method for including/excluding miracles in science. We're still waiting.

As I’ve already explained, it is not necessary to include/exclude miracles (using Rene Descartes approach, for example). The evolutionist continues:

Without that all you are giving us is meaningless complaining.

Meaningless complaining? Evolutionists violate scientific logic, you point it out, and its dismissed as meaningless complaining. As I pointed out here, the evolutionary claims are not scientific. Evolutionists can modify their approach and join science, or just blame the messenger and continue with their metaphysics.

Sunday, July 10, 2011

Here is a NatureNews Feature that speaks volumes about the state of evolutionary theory. It explains how the Human Genome project and high throughput technologies have revealed levels of complexity evolutionists hadn’t even dreamed of. It is yet another monumental failure of evolutionary theory, even though we all know evolution is a fact.

Not that long ago, biology was considered by many to be a simple science, a pursuit of expedition, observation and experimentation. At the dawn of the twentieth century, while Albert Einstein and Max Planck were writing mathematical equations that distilled the fundamental physics of the Universe, a biologist was winning the Nobel prize for describing how to make dogs drool on command.

And yet life scientists such as Joseph LeConte were absolutely certain evolution was true. They did not have the foggiest notion of how the biological world could have arisen on its own. In fact they didn’t understand much about the biological world period. But that never got in the way of their certainty.

The molecular revolution that dawned with the discovery of the structure of DNA in 1953 changed all that, making biology more quantitative and respectable, and promising to unravel the mysteries behind everything from evolution to disease origins. The human genome sequence, drafted ten years ago, promised to go even further, helping scientists trace ancestry, decipher the marks of evolution and find the molecular underpinnings of disease, guiding the way to more accurate diagnosis and targeted, personalized treatments. The genome promised to lay bare the blueprint of human biology.

Few predicted, for example, that sequencing the genome would undermine the primacy of genes by unveiling whole new classes of elements — sequences that make RNA or have a regulatory role without coding for proteins. Non-coding DNA is crucial to biology, yet knowing that it is there hasn't made it any easier to understand what it does. "We fooled ourselves into thinking the genome was going to be a transparent blueprint, but it's not," says Mel Greaves, a cell biologist at the Institute of Cancer Research in Sutton, UK.

Translation: Evolution’s simplistic, gene-centric, just-add-water view of biology led researchers to believe that sequencing the entire genome would lead to great breakthroughs. That naïve view became yet another failed evolutionary expectation.

Instead, as sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set — a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary.

With the ability to access or assay almost any bit of information, biologists are now struggling with a very big question: can one ever truly know an organism — or even a cell, an organelle or a molecular pathway — down to the finest level of detail?

I once debated an evolutionist who said the purpose of science is to explain, and that evolution explains biology. False. As usual it is the exact opposite. Evolution does not explain biology. Evolution is constantly surprised by scientific findings.

"It seems like we're climbing a mountain that keeps getting higher and higher," says Jennifer Doudna, a biochemist at the University of California, Berkeley. "The more we know, the more we realize there is to know."

Isn’t evolution amazing?

"The crux of regulation," says the 1997 genetics textbook Genes VI (Oxford Univ. Press), "is that a regulator gene codes for a regulator protein that controls transcription by binding to particular site(s) on DNA."

Just one decade of post-genome biology has exploded that view. Biology's new glimpse at a universe of non-coding DNA — what used to be called 'junk' DNA — has been fascinating and befuddling.

In the past few years the story of regulation has become profoundly more complex than evolutionists ever imagined. Needless to say, there is no credible, scientific, explanation for how it all evolved.

Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. "Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naive," says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia.

Indeed. It is also “incredibly naïve” to insist we know how such complexity arose.

Even for a single molecule, vast swathes of messy complexity arise. The protein p53, for example, was first discovered in 1979, and despite initially being misjudged as a cancer promoter, it soon gained notoriety as a tumour suppressor — a 'guardian of the genome' that stifles cancer growth by condemning genetically damaged cells to death. Few proteins have been studied more than p53, and it even commands its own meetings. Yet the p53 story has turned out to be immensely more complex than it seemed at first.

In 1990, several labs found that p53 binds directly to DNA to control transcription, supporting the traditional Jacob–Monod model of gene regulation. But as researchers broadened their understanding of gene regulation, they found more facets to p53. Just last year, Japanese researchers reported3 that p53 helps to process several varieties of small RNA that keep cell growth in check, revealing a mechanism by which the protein exerts its tumour-suppressing power.

Even before that, it was clear that p53 sat at the centre of a dynamic network of protein, chemical and genetic interactions. Researchers now know that p53 binds to thousands of sites in DNA, and some of these sites are thousands of base pairs away from any genes. It influences cell growth, death and structure and DNA repair. It also binds to numerous other proteins, which can modify its activity, and these protein–protein interactions can be tuned by the addition of chemical modifiers, such as phosphates and methyl groups. Through a process known as alternative splicing, p53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development. In fact, it seems wilfully ignorant to try to understand p53 on its own. Instead, biologists have shifted to studying the p53 network, as depicted in cartoons containing boxes, circles and arrows meant to symbolize its maze of interactions.

Of course beyond just-so stories, evolutionists have no idea how such complexity evolved. And yet p53 is just one example of biology’s complexity that defies evolution.

And reading further it is good to see a point of agreement:

The p53 story is just one example of how biologists' understanding has been reshaped, thanks to genomic-era technologies. Knowing the sequence of p53 allows computational biologists to search the genome for sequences where the protein might bind, or to predict positions where other proteins or chemical modifications might attach to the protein. That has expanded the universe of known protein interactions — and has dismantled old ideas about signalling 'pathways', in which proteins such as p53 would trigger a defined set of downstream consequences.

"When we started out, the idea was that signalling pathways were fairly simple and linear," says Tony Pawson, a cell biologist at the University of Toronto in Ontario. "Now, we appreciate that the signalling information in cells is organized through networks of information rather than simple discrete pathways. It's infinitely more complex."

Indeed, those networks of information are “infinitely more complex” than expectations. That is hardly surprising given that those expectations came from evolutionary theory. What the data are revealing is nothing like what evolution expected.

But even with the deluge of data being provided by high-throughput technologies and the power of super computers will not easily solve biology’s infinite complexity:

In the heady post-genome years, systems biologists started a long list of projects built on this strategy, attempting to model pieces of biology such as the yeast cell, E. coli, the liver and even the 'virtual human'. So far, all these attempts have run up against the same roadblock: there is no way to gather all the relevant data about each interaction included in the model.

In many cases, the models themselves quickly become so complex that they are unlikely to reveal insights about the system, degenerating instead into mazes of interactions that are simply exercises in cataloguing.

In retrospect, it was probably unrealistic to expect that charting out the biological interactions at a systems level would reveal systems-level properties, when many of the mechanisms and principles governing inter-and intracellular behaviour are still a mystery, says Leonid Kruglyak, a geneticist at Princeton University in New Jersey. He draws a comparison to physics: imagine building a particle accelerator such as the Large Hadron Collider without knowing anything about the underlying theories of quantum mechanics, quantum chromodynamics or relativity. "You would have all this stuff in your detector, and you would have no idea how to think about it, because it would involve processes that you didn't understand at all," says Kruglyak. "There is a certain amount of naivety to the idea that for any process — be it biology or weather prediction or anything else — you can simply take very large amounts of data and run a data-mining program and understand what is going on in a generic way."

A certain amount of naivety? But if all of biology arose from those random mutations and the like, shouldn’t biology be easy to understand?

Some, such as Hiroaki Kitano, a systems biologist at the Systems Biology Institute in Tokyo, point out that systems seem to grow more complex only because we continue to learn about them. "Biology is a defined system," he says, "and in time, we will have a fairly good understanding of what the system is about."

So biology’s complexity is just an illusion of too much knowledge. Once we figure all this out we’ll see how simple it actually is. Sounds like another prediction of evolution. Will it follow the trend of its failed predecessors?

Mina Bissell, a cancer researcher at the Lawrence Berkeley National Laboratory in California, says that during the Human Genome Project, she was driven to despair by predictions that all the mysteries would be solved. "Famous people would get up and say, 'We will understand everything after this'," she says. "Biology is complex, and that is part of its beauty." She need not worry, however; the beautiful patterns of biology's Mandelbrot-like intricacy show few signs of resolving.

Yet another failed prediction.

The notion that all of this evolved into existence is outrageous. It violates both simple common sense and detailed analysis, and makes mockery of science. When will taxpayers stop funding this religious drivel?

Saturday, July 9, 2011

New research is providing a fascinating new perspective on fine-tuning and a three hundred year old debate. First for the context. When Isaac Newton figured out how the solar system worked he also detected a stability problem. Could the smooth-running machine go unstable, with planets smashing into each other? This is what the math indicated. But on the other hand, we’re still here. How could that be?

According to the Whig historians, Newton, a theist, solved the problem by invoking a divine finger. God must occasionally tweak the controls to keep things from getting out of control. It explained why the solar system hasn’t come to ruin, and it provided a role for divine providence which, otherwise, might not be needed for the cosmic machine that ran on its own.

About a century later, Whig history tells us, the French mathematician and scientist Pierre Laplace solved the stability problem when he figured out that Newton’s bothersome instabilities would iron themselves out over the long run. The solar system was inherently stable after all, with no need of divine adjustment, thank you.

Newton’s sin was to use god to plug a gap in our knowledge. What a terrible idea. First, using god to plug gaps is a science-stopper. Why investigate further if god fixes the tough problems? And second, it damages our faith when science eventually solves the problem and the divine role is further diminished. The key to avoiding this problem is to sequester religious thinking to its proper role. Science and religion must be separated lest both be damaged.

That’s the Whig history. Now for what actually happened. Instead of Newton being wrong and Laplace being right it was, as usual, the exact opposite. Newton was right and Laplace was wrong, though the problem is far more complex than either man understood.

And Newton was not the doctrinaire and Laplace was not the savior as the Whigs describe. Again, the truth would be closer to the exact opposite. Newton was more circumspect than is told, and Laplace didn’t actually solve the problem. True, he thought he had solved the problem, but his claim may indicate more about evolutionary thinking than anything to do with science.

And Newton’s allowing for divine creation and providence never shut down scientific inquiry. If that were the case he never would have written the greatest scientific treatise in history.

After Newton, the brightest minds were all over the problem of solar system stability (though it is a difficult problem and would take many years to even get the wrong answer). And no one’s faith was shattered when Laplace produced his incredibly complicated calculus solution because they were banking on some Newtonian interventionism.

But what did raise tempers was the very thought of God not only creating a system in need of repair, but then stooping so low as to adjust the controls of the errant machine. The early evolutionary thinker and Newton rival, Gottfried Leibniz found the idea more than disgraceful. The Lutheran intellectual accused Newton of disrespect for God in proposing the idea the God was not sufficiently skilled to create a self-sufficient clockwork universe.

The problem with Newton’s notion of divine providence was not that it is a science stopper (if anything such thinking spurs on scientific curiosity) or a faith killer when solutions are found. The problem is that it violates our deeply held gnosticism, which is at the foundation of evolutionary thought.

Darwin and later evolutionists have echoed Leibniz’ religious sentiment time and again. Everyone knew what the “right answer” was, and this was the cultural-religious context in which Laplace worked.

Indeed, Laplace’s “proof” for his Nebular Hypothesis of how the solar system evolved came right out of this context and was, not surprisingly, metaphysical to the core. You can read more about that here.

Today the question of the solar system’s stability remains a difficult problem. It does appear, however, that its stability is a consequence of some rather fine-tuning. Fascinating new research seems to add to this story. The new results indicate that the solar system could become unstable if diminutive Mercury, the inner most planet, enters into a dance with Jupiter, the fifth planet from the Sun and the largest of all. The resulting upheaval could leave several planets in rubble, including our own.

Using Newton’s model of gravity, the chances of such a catastrophe were estimated to be greater than 50/50 over the next 5 billion years. But interestingly, accounting for Albert Einstein’s minor adjustments (according to his theory of relativity), reduces the chances to just 1%.

Like so much of evolutionary theory, this is an intriguing story because not only is the science interesting, but it is part of a larger confluence involving history, philosophy and theology.